[gmx-users] question about energy and pressure

[Mark Abraham]

Qiao Baofu wrote:
> Hi all,
> 
> I have some questions about the gromacs:
> 
> 1. I simualted a pure small molecule system. All the simulation is ok. 
> But when I use g_energy to calculate the energy of bond, angle, lj, and 
> coloumb, it gives the following energy. The energies is much bigger, 
> about 50-100 times bigger than the reported data.  What's wrong?

What is this "reported data"?

> Statistics over 5000001 steps [ 0.0000 thru 5000.0000 ps ], 6 data sets
> 
> Energy                      Average       RMSD     Fluct.      Drift  
> Tot-Drift
> ------------------------------------------------------------------------------- 
> 
> Bond                        2869.13    93.6564    93.6562 0.000137548   
> 0.687742
> Angle                       7303.46     140.13     140.13 0.000189867   
> 0.949334
> Ryckaert-Bell.          3326.2    97.6245    97.6161 -0.000890977   -4.45489
> LJ-(SR)                   -7616.62    138.684     138.67 -0.00138166   
> -6.90831
> Coulomb-(SR)        -22763.2    138.465    138.238 -0.00549019    -27.451
> Potential                  -64743     219.54    219.203 -0.00842365   
> -42.1182
> 
> 2. I used the "isotropic!!" pressure coupling, but at the end of the 
> .log file (in the average section), it says:
> 
>  Pressure (bar)
>    -2.64364e+01    3.71622e+01     3.00738e+00
>     3.71622e+01    1.32932e+01   -2.49814e+01
>     3.00738e+00   -2.49814e+01    1.61609e+01
> 
> The Pxx, Pyy, Pzz are not equal. Why?

What is the geometry of your system?

Mark